The output from HLAminer, DQA1*03 01P, is a P-designation annotation [ 30] that groups DQA1*03 01, DQA1*03 03 and a few other alleles.
Additional file 1: Table S1 presents the full name, designation and annotation of each gene.
Genes that shared the same annotation designation were determined to be isozymes while those with different names were seen to be subunits of a protein.
There were 25 bicupins that were divided into three clusters corresponding to the annotation designations at SWISS-PROT: glutelin precursor proteins, globulin-1 proteins, and 12S seed storage proteins (as shown in Supplementary Table 1).
The subsystem and protein function designation were determined through annotation with RAST [ 23] with the exception of the proteins annotated as antibiotic biosynthesis monooxygenonase which was designated by Blast2GO [ 24].
We designers love annotations.
For telomeric sequence designation, we used the annotations for each chromosome from the Saccharomyces Genome Database [15].
In the past, several authors published sequences of Tribolium CSPs and OBPs based on computational predictions [ 7, 17, 21, 65] resulting in different conflicting annotations and designation.
Whenever possible the proposed new nomenclature conserves the original letter designations used in previous annotation e.g. RipP1 is PopP1 [ 19]; RisPopP2 PopP2 [ 20]; RipAA is AvrA [ 31].
Approximately 90% of the 3115 core genes clustered with orthologs sharing identical COG designations suggesting our automated annotation pipeline was accurate.
Probable Arabidopsis orthologues, MIPS designations, KOG#, GO annotations, and BLASTX hits were determined for these probes when possible (see Additional file 1).
